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Yorodumi- PDB-219d: DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 219d | ||||||
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Title | DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT) (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE MOIETY | ||||||
Components |
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Keywords | DNA-RNA HYBRID / DNA / RNA / HYBRID / PHOSPHOROTHIOATE / DNA-RNA COMPLEX | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Gonzalez, C. / James, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints. Authors: Gonzalez, C. / Stec, W. / Reynolds, M.A. / James, T.L. #1: Journal: Biochemistry / Year: 1994 Title: Structural Study of a DNA(Dot)RNA Hybrid Duplex with a Chiral Phosphorothioate Moiety by NMR: Extraction of Distance and Torsion Angle Constraints and Imino Proton Exchange Rates Authors: Gonzalez, C. / Stec, W. / Kobylanska, A. / Hogrefe, R.I. / Reynolds, M.A. / James, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 219d.cif.gz | 19.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb219d.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 219d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 219d_validation.pdf.gz | 305.7 KB | Display | wwPDB validaton report |
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Full document | 219d_full_validation.pdf.gz | 305.5 KB | Display | |
Data in XML | 219d_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 219d_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/19/219d ftp://data.pdbj.org/pub/pdb/validation_reports/19/219d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3100.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
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#2: RNA chain | Mass: 3121.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: RIBONUCLEIC ACID |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY MINOR ...Text: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REPRESENT THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE SIXTH ROOT R-FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL NOE DATA, CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND JAMES), HAS A VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION BETWEEN EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING CONSTRAINTS IS 2.01 HZ. THIS POOR FIT OF THE COUPLING CONSTANTS IS DUE TO CONFORMATIONAL FLEXIBILITY IN THE SUGAR RING. |
-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Software | Name: AMBER / Classification: refinement |
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NMR software | Name: AMBER4 / Developer: PEARLMAN,KOLLMAN / Classification: refinement |
Refinement | Method: molecular dynamics / Software ordinal: 1 Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 |
NMR ensemble | Conformers submitted total number: 1 |